Udział metabolizmu RNA
w procesach fizjologicznych:
rozwój i odpowiedź na stres
Anna Golisz
Levels of regulation
I. Chromatin and transcription
II. RNA processing: pre-mRNA splicing
(alternative splicing - AS) and 3’ formation III. RNA stability
IV.Regulation via microRNA
RNA metabolism regulates most of developmental and signaling processes in plants
► Germination
► Circadian clock
► Transition from vegetative to generative development
► Flowering
► Stress response
Regulation of plant metabolism
I. Chromatin and transcription
Plant clocks control a plethora of biological processes
2000, vol. 5, no. 12
The central oscillator
1) CCA1 – CIRCADIAN CLOCK ASSOCIATED 1 LHY – LATE ELONGATED HYPOCOTYL
MYB transcription factors
reduction in mRNA levels: negative feedback loop
mRNA level peaking at dawn
2) TOC1 – TIMING OF CAB EXPRESSION 1
TOC1 expression oscillates peaking during early evening
(opposite to CCA1 and LHY)
Stratmann & Mas, Seminars in Cell & Developmental Biology (2008) 554–559
Chromatin-dependent regulation of TOC1
Stratmann & Mas, Seminars in Cell & Developmental Biology 19 (2008) 554–559
HAT – histone acetyltransferase
HDAC – histone deacetylase
Model for a feedback loop involving LHY, CCA1 and TOC1
3) LHY, CCA1 repress expression of TOC1, their positive regulator
1) PHY and CRY as photoreceptors 2) LHY, CCA1 and TOC1 negative feedback loop
4) Generation of circadian rhythms, including that of CO (CONSTANTS) for flowering time
5) ELF3 (early flowering3) gates the light signals, resetting it at dawn
6) ZTL (ZEITLUPE) and GI (GIGANTEA) also act on light input
FT – FLOWERING LOCUS T
2003, 6:13-19
Flowering
pathway in plant
Flowering I-II.
Chromatin
and RNA
processing
Pathways controlling flowering time in A. thaliana
Int. J. Dev. Biol. 2005, 49: 773-780
Functions of antisense RNAs in the regulation of plant flowering
Rosonina and Manley, Dev. Cell, 2010 Hornyik et al.. RNA UK, 2010
FLC – Flowering Locus C
− MADS box transcription factor
− major repressor of flowering in plants
− expression regulated by FLC antisense
► two major forms of FLC antisense are synthesized
► regulated by alternative polyadenylation by RNA binding proteins, FPA and FCA, and CTSF factor FY
► short asFLC (3’ processing at site I) recruits histone demethylase FLD which introduces transcriptionally repressive histone modifications leading to FLC silencing
► long asFLC (3’ processing at site II) causes nucleosomal rearrangements at
the FLC promoter leading to FLC transcription
Convergence points in abiotic and biotic stress signaling networks
Fujita et al. Current Opinion in Plant Biology 2006, 9:436–442
I and III. Transcription and RNA stability
Stress response
Phytohormones – old timers and newcomers
Auxin
Cytokinin Gibberellin
Abscisic Acid
Ethylene
Brassinosteroid Salicylic Acid
Jasmonic Acid
Strigolactone
Phytohormones regulate all stages of the plant life cycle
Fertilization and fruit formation
Seed
dormancy Embryogenesis
Fruit ripening
Germination
Flower
development
Growth and
branching
Hormonal responses to abiotic stress
Photooxidative stress
High temperature stress
Water deficit, drought Soil salinity
Air pollution
Wounding and
mechanical damage
Cold and
freezing stress
Plants’ lives are very stressful...
ABA and ethylene help plants respond
to stress
Reprinted by permission from Macmillan Publishers, Ltd. Nature Chemical Biology. Vickers, C.E., Gershenzon, J., Lerdau, M.T., and Loreto, F. (2009) Nature Chemical Biology 5: 283 - 291
Adapted with permission from RIKEN
Seed quality
Stress tolerance
Dormancy Germination
Biotic stress response
Stomatal aperture Gene expression
Development
Abscisic Acid
controls many plant processes including stress responses, development and reproduction
ABSCISIC ACID (ABA)
ABA synthesis is strongly induced in response to stress
R.L. Croissant, , Bugwood. www.forestryimages.org . Zabadel, T. J. Plant Physiol. (1974) 53: 125-127.
ABA levels rise during drought stress due in part to increased biosynthesis
Hours of drought stress
Leaf water potential
(atm)
[ABA]
µg/g dry weight
Abscisic acid (ABA) signaling pathway
Sheard and Zheng NATURE Vol 462/3 December 2009
There are many genes encoding PYR/PYL/RCARs
Common Name Species Number of genes
Soybean Glycine max 23
Corn Zea mays 20
Western poplar Populus
trichocarpa 14
Rice Oryza sativa 11
Grape Vitis vinifera 8
Sorghum Sorghum bicolor 8
Barrel medic (a model legume)
Medicago
truncatula 6
Arabidopsis Arabidopsis
thaliana 14
Klingler, J.P., Batelli, G., and Zhu, J.-K. J. Exp.Bot. 61: 3199-3210
Raghavendra, A.S., Gonugunta, V.K., Christmann, A., and Grill, E. (2010) Trends Plant Sci. 15: 395-401.
The 14 PYR/RCARs in Arabidopsis
Schematic model of the transcriptional regulation of ABA signaling by AREB/ABF and ABI5 family TFs
Fujita et al. 2011 J Plant Res
ahg2-1 – ABA hypersensitive germination
poly(A)-specific ribonuclease AtPARN deadenylation, mRNA degradation
lba1 – ABA-hypersensitive seed germination
RNA helicase UPF1 Nonsense-Mediated decay (NMD) Nonsense-Mediated mRNA decay
sad1 – supersensitive to ABA and drought
LSM complex (Sm-like) snRNP proteins mRNA splicing and degradation
ABA response in RNA metabolic mutants
hyl1 – hypersensitive to salt and ABA RNA binding protein HYL1
miRNA processing and accumulation los4 – sensitive to ABA and cold
putative DEAD box RNA helicase LOS4 mRNA export
m
7G
Lsm1-7
m
7G
PARN
abh1 – hypersensitive response to ABA in germination inhibition nuclear cap-binding protein CBP80
mRNA splicing and stability
ABA response involves RNA processing and
degradation systems
Hirayama&Shinozaki 2007 TRENDS in Plant Science
Ethylene (C 2 H 4 ) is a gaseous hormone with diverse actions
Ethylene regulates:
fruit ripening
organ expansion
senescence
gene expression
stress responses
Cotton plants
7 days ethylene Air (control)
Air Ethylene
Arabidopsis
Beyer, Jr., E.M. (1976) Plant Physiol. 58: 268-271.
Ethylene responses in Arabidopsis
Lorenzo, O., Piqueras, R., Sanchez-Serrano, J.J., and Solano, R. (2003). Plant Cell 15: 165-178;
Rüžička, K., Ljung, K., Vanneste, S., Podhorská, R., Beeckman, T., Friml, J., and Benková, E. (2007). Plant Cell 19: 2197-2212.
Inhibition of leaf cell expansion
Acceleration of leaf senescence Ethylene-induced gene expression
Inhibition of root
elongation
=XRN4
Ethylene signal transduction pathway:
XRN4 - 5’-3’ cytoplasmic exoribonuclease
Olmedo et al. PNAS 2006 vol. 103 no. 36
miRNAs and vegetative phase change
Germination
zygote
JUVENILE PHASE
Vegetative phase change
Vegetative phase change is the transition from juvenile to adult growth in plants
ADULT PHASE
REPRODUCTIVE PHASE EMBRYONIC
PHASE
IV. Regulation via miRNA
►Small RNAs are a pool of 21 to 24 nt RNAs that generally function in gene silencing
►Small RNAs contribute to post- transcriptional gene silencing by affecting mRNA translation or stability
►Small RNAs contribute to
transcriptional gene silencing through epigenetic modifications to chromatin
AAAAA
RNA Pol Histone modification, DNA methylation
What are small RNAs?
Leaves are modulated by miRNA activity throughout development
Pulido, A., and Laufs, P. (2010). J.Exp.Bot. 61: 1277-1291
M.W. Jones-Rhoades et al. Annu. Rev. Plant Biol. 2006. 57:19–53
Phenotypes resulting from microRNA (miRNA) overexpression in Arabidopsis
miRNA156
miRNA164
miRNA172
miRNA319
miRNA166
miRNA159a
miRNA160
Phase change is specified by miRNAs
HASTY, with a shortened juvenile phase, encodes a protein needed for miRNA
export from nucleus to cytoplasm hasty
Loss-of-function zippy mutants prematurely express adult vegetative traits. ZIPPY
encodes an ARGONAUTE protein, AGO7
Wild-type zippy
Bollman, et al. (2003) Development 130: 1493-1504 Hunter et al. (2003) Curr. Biol. 13: 1734–1739
WT hasty
WT zippy
Poethig, R.S. (2009) Curr. Opin. Genet. Devel.
miR156 overexpression prolongs juvenile
phase in Arabidopsis
Reciprocal expression patterns of
MIR156 and MIR172 in the juvenile and adult phase of development
Chuck et al. Current Opinion in Plant Biology 2009, 12:81–86
miR172 expression temporally regulates AP2-like proteins
It is thought that floral initiation can
occur when the level of AP2-like
floral inhibitors drops below a
certain level
Aukerman, M.J., and Sakai, H. (2003) Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-Like target genes Plant Cell 15: 2730-2741.
WT mutant
ap2-12
Role of conserved plant miRNAs
Khraiwesh et al. 2011 Biochimica et Biophysica Acta
Regulation of miRNA and their target genes by ABA and salt stress in Arabidopsis
Plant Mol Biol (2009) 71:51–59
The Plant Journal (2007) 49, 592–606
Khraiwesh et al. 2011 Biochimica et Biophysica Acta
green boxes – upregulated small RNA,
light green boxes – slightly upregulated small RNA red boxes – downregulated small RNA
Stress-regulated small RNAs and their target families
Regulatory network of stress-responsive miRNAs in Arabidopsis
B. Khraiwesh et al. Biochimica et Biophysica Acta 1819 (2012) 137–148
Distinctions between animal and plant miRNAs
Animal miRNAs Plant miRNAs
conserved miRNA precursors less conserved mature miRNA pri-miRNA cleaved by DICER
produce 60-70 nt pre-miRNA
pri-miRNA cleaved by Dicer-like1 (DCL1) produce 60-300 nt
miRNA precursor cleaved to miRNA duplex in the
cytoplasm
cleaved to miRNA duplex in the nucleus
miRNA duplex is exported from the nucleus by Exportin-5
miRNA duplex is exported from the nucleus by HASTY (HST) homolog Exportin-5
Lu & Huang BBRC 2008, 368, 458-462
Wienholds, Plasterk FEBS Letters 579 (2005) 5911–5922
Biological function of miRNAs in animal and disease
miRNA – control of differentation and development of mammalian cells
Neuronal
differentiation Muscle cell differentation
Cell development
Stefani G., Slack F. J., (2008) Mol Cell Biol
miRNAs regulate developmental timing
miRNAs were discovered in studies of developmental
progressions in the nematode C. elegans.
A miRNA encoded by lin-4 is required for proper larval
development.
lin-14 gene
3’ untranslated region
lin-4 binding sites
Lee, R.C., Feinbaum, R.L., and Ambrose, V. (1993). Cell 75: 843–845.
Wightman, B., Ha, I., and Ruvkun, G. (1993). Cell 75: 855–862.
lin-14 mRNA lin-4 miRNA
Downregulation of lin-14 by lin-4 is necessary for normal development
Wild-type C. elegans
lin-4 Loss-of-function lin-4 is a negative
regulator of lin-14 In wild-type worms,
lin-14 is expressed early and then shut off.
lin-14 expression
lin-4 loss-of- function
causes lin-14 expression to remain high.
Lee, R.C., Feinbaum, R.L., and Ambrose, V. (1993). Cell 75: 843–845.
Wightman, B., Ha, I., and Ruvkun, G. (1993). Cell 75: 855–862.
CurrentOpinioninGenetics&Development 2011, 21:491–497
Regulation of dendritic spine morphogenesis by microRNAs
miR-134 and miR-138 – reduced dendritic spine volume miR-132 – increased dendritic spine density
miR-125 – decreased dendritic spine width and increased length
► Several miRNAs
(miR183/96/182, miR204, miR211)
are transcriptionally upregulated by light in mouse retinal neurons
► Glutamate transporter SLC1A1 (voltage-dependent) is one of the targets of the light- regulated miRNAs
► miRNAs in retinal neurons decay much faster than in nonneuronal cells
► Blocking action potentials or glutamate receptors
strongly affects miRNA turnover
Light-Regulated Retinal MicroRNAs
Filipowicz et al. Cell 2010, 141, 618-631
microRNA metabolism in neurons is higher than in most other cells types
miRNA as a DECOY in myeloid cell differentiation
Beitzinger and Meister, Cell, 2010
► RNA binding protein hnRNP E2
(activated by BCR/ABL kinase in chronic myeloid leukemia patients-CML) inhibits translation of C/EBP mRNA by binding to its 5’ UTR. This stops MD
► miR-328 directly binds hnRNP E2 due to sequence similarity to the E2 binding site on C/EBP mRNA
► translation of C/EBP is activated leading to MD
► C/EBP stimulates miR-328
transcription (positive feedback loop for MD
fine-tuning)
ncRNAs and disease
Prasanth and Spector, GeneDev, 2007